Neanderthal DNA Sequencing

In July of 1997 the first ever sequencing of Neanderthal DNA, a
breakthrough in the study of modern human evolution, was announced in
the Journal Cell (Krings, et. al., 1997). DNA was extracted
for the type specimen and the mitochondrial DNA (mtDNA) sequence was
determined. This sequence was compared to living human mtDNA sequences
and found to be outside the range of variation in modern humans. Age
estimation of the Neanderthal and human divergence is four times older
than the age of the common mtDNA ancestor of all living humans. The
authors suggest that the Neanderthals went extinct without contribution
to the present mtDNA of modern humans.

The Neanderthals inhabited Europe from about 300,000 to 30,000 years
ago. Previous hypotheses that Neanderthals were replaced relied on mtDNA
study of existing populations. Directly analyzing the remains of the
Neanderthal type specimen has affirmed this view.

The researchers removed a sample from the humerous specimen. They analyzed
the extend of amino acid racemization to determine suitability for analysis.
It was determined that the amino acid levels were at 20% to 73% of those
in modern bone, evidencing DNA survival. This and other tests indicated
the remains might contain amplifiable DNA. Amplification products were
cloned. Twenty seven clones of obvious non-human origin were produced.
The entire sequence of hypervariable region 1 was determined, 387 positions.
This was accomplished with overlapping segments.

In comparison to modern DNA 27 differences are seen. The Neanderthal
sequence was compared with 2051 human and 59 chimpanzee sequences over
360 base pairs. Twenty five of the 27 variable base pairs coincide with
positions that vary in at least one of the human sequences. The sequence
was compared with 994 human mtDNA lineages. While these lineages differ
among themselves by eight substitutions on average, the range of difference
with the Neanderthal sequence is 22-36. The Neanderthal sequence has
28.2 ±1.9 substitutions from the European lineage, 27.1 ±12.2 substitutions
from the African lineage, 27.7 ±2.2 substitutions from the Asian lineage,
27.4 ±1.8 substitutions from the American lineage, and 28.3 ±2.7 substitutions
from the Australian/Oceanic lineages. This indicates no closer a relationship
with Europeans than with the other modern human subsets considered.

The comparison to chimpanzees with modern humans is 55.0 ±3.0, compared
to the average between humans and Neanderthals of 25.6 ±2.2. These results
indicate a divergence of the human and Neanderthal lineages long before
the most recent common mtDNA ancestor of humans. Based on the estimated
divergence date of 4-5 million years ago for humans and chimpanzees,
the authors estimate the human and Neanderthal divergence at 550,000-690,000
years ago. The age of the common human ancestor, using the same procedure,
is about 120,000-150,000 years ago.

These results do not rule out the possibility that Neanderthals contributed
other genes to modern humans. However, the results support the hypothesis
that modern humans arose in Africa before migrating to Europe and replacing
the Neanderthal population with little or no interbreeding.

In March of 2000 the results of a second fossil Neanderthal DNA sequencing
was announced in the Journal Nature (Ovchinnikov, et. al.,
2000). The fossil specimen is an infant from the Caucasus region
dating to less than 30,000 years ago. A rib was used in the DNA isolation
and a 345 base pair sequence was produced. The specimen had 22 base
pair differences, compared to 27 for the type specimen, over the 345
base pair sequence. The two Neanderthals share 19 substitutions. Although
the two Neanderthals were separated by 2,500 km, they are closely related
in mtDNA lineages.

This second study estimates the most recent common ancestor of the
Neanderthals at 151,000-352,000 years, while the human and Neanderthal
divergence is placed at 365,00-853,000 years. The same model produces
an age for the divergence of modern humans at 106,000-246,000 years
ago.